clustered hits | time_effect | Omics-Datatype: PTX | Date-Time: 18_09_2024-11_31_09


Note!

Clustering of features that show significant changes over time (= hits).
Clustering was done based on the min-max normalized shape of the spline.
For this, the spline parameters in the limma topTable are used to generate 1000 curve datapoints between 0 and 1. These datapoints are used for hierarchical clustering.
Right-click on any plot in this report to save it as a .svg (vector graphic) file!
If one level of the experiment is not shown, it means it has < 2 hits!

feature_name "formula": {annotation-column-x}_{annotation-column-y}_ ... :
Gene_name



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Report Info ℹ

omics data type :PTX
data description :Proteomics data
data collection date :February 2024
meta condition :Phase
meta batch :Reactor,
limma design :~ 1 + Phase*X + Reactor
analyst name :Thomas Rauter
contact info :thomas.rauter@plus.ac.at
project name :DGTX
method description :NA
results summary :NA
conclusions :NA

Downloads 📥

data with annotation :
meta :
limma topTables :
Enrichr clustered genes :
Enrichr background :

Table of Contents

Exponential

Spline-type: Natural cubic spline
DoF: 2
Knots: NA
Boundary-knots: NA

adj.p-value threshold: 0.050

Number of hits: 61

Overall Clustering

Plot
Plot

Min-max normalized individual and mean splines

Plot
Plot
Plot
Plot
Plot
Plot

Z-Score of log2 Value Heatmap

Rows = features (labels on the right, cluster labels on the left), columns = timepoints; Blue = down, red = up, --> compared to the rest of the row;
Plot

Individual Significant Features (Hits) Splines

Asterisks definition:
Adj. p-value < 0.05 --> *
Adj. p-value < 0.01 --> **
Adj. p-value < 0.001 --> ***

Cluster 1 | Hits: 21

1-acylglycerol-3-phosphate O-acyltransferase 2
Plot
AHNAK nucleoprotein 2
Plot
CLOCK interacting pacemaker
Plot
CTTNBP2 N-terminal like
Plot
NPC1 like intracellular cholesterol transporter 1
Plot
WD repeat containing, antisense to TP73
Plot
acid sensing ion channel subunit 2
Plot
cell division cycle associated 3
Plot
cofilin 1
Plot
cytidine/uridine monophosphate kinase 1
Plot
family with sequence similarity 181 member A
Plot
leucine rich repeat containing 14B
Plot
lysine acetyltransferase 2A
Plot
ribonucleic acid export 1
Plot
schwannomin-interacting protein 1
Plot
serotransferrin
Plot
solute carrier family 35 member D3
Plot
sterile alpha motif domain containing 12
Plot
testis associated actin remodelling kinase 2
Plot
ubiquitin conjugating enzyme E2 U
Plot
zinc finger MIZ-type containing 2
Plot

Cluster 2 | Hits: 8

ADP ribosylation factor like GTPase 1
Plot
Coenzyme A synthase
Plot
IQ motif containing G
Plot
RB binding protein 9, serine hydrolase
Plot
aquaporin 3 (Gill blood group)
Plot
heat shock protein HSP 90-alpha-like
Plot
snRNA-activating protein complex subunit 5-like
Plot
ubiquinol-cytochrome-c reductase complex assembly factor 3
Plot

Cluster 3 | Hits: 8

BPI fold containing family B member 3
Plot
N-terminal EF-hand calcium binding protein 2
Plot
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 4-like
Plot
THAP domain containing 6
Plot
TNF receptor superfamily member 21
Plot
armadillo repeat containing 3
Plot
karyopherin subunit alpha 7
Plot
ribosomal protein S24
Plot

Cluster 4 | Hits: 16

ATP synthase membrane subunit f
Plot
ATPase plasma membrane Ca2+ transporting 3
Plot
CCHC-type zinc finger nucleic acid binding protein
Plot
ER membrane protein complex subunit 3
Plot
adhesion G protein-coupled receptor F5
Plot
chloride channel CLIC like 1
Plot
coiled-coil domain containing 60
Plot
crystallin beta A4
Plot
geranylgeranyl diphosphate synthase 1
Plot
membrane bound O-acyltransferase domain containing 4
Plot
pleckstrin homology and coiled-coil domain containing D1
Plot
small integral membrane protein 41
Plot
solute carrier family 26 member 9
Plot
striatin
Plot
tRNA aspartic acid methyltransferase 1
Plot
ubiquitin specific peptidase 19
Plot

Cluster 5 | Hits: 4

ATPase H+ transporting V1 subunit C2
Plot
core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1
Plot
phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha
Plot
zinc finger and BTB domain containing 38
Plot

Cluster 6 | Hits: 4

RNA binding protein, mRNA processing factor 2
Plot
betaine--homocysteine S-methyltransferase
Plot
mitochondrial nucleoid associated protein 1
Plot
triggering receptor expressed on myeloid cells 1
Plot

Stationary

Spline-type: Natural cubic spline
DoF: 2
Knots: NA
Boundary-knots: NA

adj.p-value threshold: 0.050

Number of hits: 5

Overall Clustering

Plot
Plot

Min-max normalized individual and mean splines

Plot
Plot
Plot

Z-Score of log2 Value Heatmap

Rows = features (labels on the right, cluster labels on the left), columns = timepoints; Blue = down, red = up, --> compared to the rest of the row;
Plot

Individual Significant Features (Hits) Splines

Asterisks definition:
Adj. p-value < 0.05 --> *
Adj. p-value < 0.01 --> **
Adj. p-value < 0.001 --> ***

Cluster 1 | Hits: 3

S100 calcium binding protein G
Plot
ribosomal protein S24
Plot
trinucleotide repeat containing 18
Plot

Cluster 2 | Hits: 1

hemojuvelin BMP co-receptor
Plot

Cluster 3 | Hits: 1

SEC61 translocon subunit alpha 2
Plot